Quality Filters

The Quality Filters allow one to filter variants by variant quality metrics. The filter can operate in a Simple or Advanced mode.

Simple mode

Select a minimum degree of sequencing Quality (Low, Moderate, High).

Advanced mode

For SNVs and Indels:

• Select a minimum degree of sequencing Quality (Low, Moderate, High),

• Define minimum Mapping Quality (0-60 - value can be exceeded using the text box),

• Specify minimum Depth (0-500 - value can be exceeded using the text box),

• Set minimum number of alternate reads in Alternate Read (0-500 - value can be exceeded using the text box). ***Note:***available for cases run with pipeline version 5.26+.

• Set limits on Allele bias (0-100). ***Note:***when applied to mtDNA variants, the Allele bias filter operates on heteroplasmy levels.

For CNVs:

• Set limits on CNV Length (50bp, 1kb, 10kb, 100kb, 1Mb, 100Mb, Max CNV length),

• Set minimum CNV Bin Count (1, 5, 10, 25, 50, 100, 500).

Default values

When Filters are Reset to Default, The Quality Filters are set to:

• Quality: Moderate and High,

• Mapping Quality ≥45,

• Depth ≥ 10,

• Alternate Read - no filtering,

• Allele bias - no filtering,

• CNV Length - no filtering,

• CNV Bin Count - no filtering.

As of version 2.26: